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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ) $local_species = 'cfa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ) $local_species = 'cfa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ), 'gf_id' => 'HOM05D001223', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001223' ), 'data_identifier' => 'HOM05D001223', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001223', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '509', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21770' => 'bna', 'A06p04860' => 'bna', 'A07p19180' => 'bna', 'A08p35500' => 'bna', 'A09p66200' => 'bna', 'Aa31LG5G7530' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1503' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1775' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1777' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1792' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2046__2047' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2048' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3631' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3814' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.513' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.579' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3896' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3899' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4346' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4349' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4502' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1440' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2538' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.267' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.272' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.277' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.282' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.285' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.317' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.319' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3871' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3881' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4082' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.5075' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2041' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2011' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2014' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2028' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3354' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.602' => 'aag', 'Actinidia00205' => 'ach', 'Actinidia07072' => 'ach', 'Actinidia07073' => 'ach', 'Actinidia20462' => 'ach', 'Actinidia20463' => 'ach', 'Actinidia26690' => 'ach', 'Actinidia26691' => 'ach', 'Actinidia37247' => 'ach', 'Actinidia37248' => 'ach', 'Actinidia39038' => 'ach', 'Actinidia39039' => 'ach', 'Ah.08g214880' => 'amhyb', 'Ah.10g031920' => 'amhyb', 'Ah.15g096820' => 'amhyb', 'AL1G18030' => 'aly', 'AL4G23220' => 'aly', 'Aqoxy301s002' => 'aox', 'Aqoxy3G00888' => 'aox', 'Aqoxy3G03458' => 'aox', 'Aqoxy3G03459' => 'aox', 'Aqoxy4G01599' => 'aox', 'Aqoxy4G01665' => 'aox', 'Aqoxy4G01752' => 'aox', 'Aqoxy4G02810' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B8VHIV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQM6WK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1I4C8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q700U9' => 'arhy', 'AT1G07750' => 'ath', 'AT2G28680' => 'ath', 'ATR0807G206' => 'atr', 'Atru.chr10.1173' => 'acertr', 'Atru.chr2.1856' => 'acertr', 'Atru.chr2.1857' => 'acertr', 'Atru.chr2.1862' => 'acertr', 'Atru.chr3.3809' => 'acertr', 'AUR62002332' => 'cqu', 'AUR62008436' => 'cqu', 'AUR62009632' => 'cqu', 'AUR62014951' => 'cqu', 'AUR62021655' => 'cqu', 'AUR62021657' => 'cqu', 'AUR62023856' => 'cqu', 'AUR62028564' => 'cqu', 'AUR62029187' => 'cqu', 'AUR62033519' => 'cqu', 'AUR62040540' => 'cqu', 'BcaB02g06706' => 'bca', 'BcaB02g10191' => 'bca', 'BcaB03g13132' => 'bca', 'BcaB03g13377' => 'bca', 'BcaB06g28241' => 'bca', 'BcaC02g08146' => 'bca', 'BcaC02g10991' => 'bca', 'BcaC07g41977' => 'bca', 'BcaC07g41978' => 'bca', 'BcaC07g42496' => 'bca', 'BolC4t23757H' => 'bol', 'BolC4t27308H' => 'bol', 'BolC4t27311H' => 'bol', 'BolC5t29343H' => 'bol', 'BolC5t34645H' => 'bol', 'BolC8t47127H' => 'bol', 'BolC8t49597H' => 'bol', 'BolC8t52565H' => 'bol', 'BraA04t17743Z' => 'bra', 'BraA06t23690Z' => 'bra', 'BraA07t29625Z' => 'bra', 'BraA08t35456Z' => 'bra', 'BraA09t41958Z' => 'bra', 'C04p22410' => 'bna', 'C04p57880' => 'bna', 'C05p05740' => 'bna', 'C05p59910' => 'bna', 'C08p03310' => 'bna', 'C08p16730' => 'bna', 'C08p19640' => 'bna', 'C08p50370' => 'bna', 'CAN.G1057.7' => 'can', 'CAN.G668.5' => 'can', 'CAN.G798.4' => 'can', 'CAN.G820.6' => 'can', 'CAN.G820.7' => 'can', 'CANSAT78G2293' => 'cansat', 'CANSAT78G2410' => 'cansat', 'CARHR007580' => 'chi', 'CARHR121790' => 'chi', 'Carub.0001s0713' => 'cru', 'Carub.0004s0968' => 'cru', 'Carub.0005s0869' => 'cru', 'Ca_17821_v3' => 'car', 'Ca_17822_v3' => 'car', 'Ca_19198_v3' => 'car', 'CBR_g40947' => 'cbr', 'CBR_g40949' => 'cbr', 'CBR_g40951' => 'cbr', 'CBR_g40952' => 'cbr', 'CBR_g40953' => 'cbr', 'CBR_g40959' => 'cbr', 'CBR_g40965' => 'cbr', 'CBR_g40968' => 'cbr', 'CBR_g41651' => 'cbr', 'CBR_g44481' => 'cbr', 'CBR_g44483' => 'cbr', 'CBR_g44484' => 'cbr', 'CBR_g50768' => 'cbr', 'CBR_g54015' => 'cbr', 'CBR_g9002' => 'cbr', 'CBR_g9003' => 'cbr', 'CBR_g9005' => 'cbr', 'Cc00_g29390' => 'ccan', 'Cc01_g12220' => 'ccan', 'Cc02_g22570' => 'ccan', 'Cc02_g32380' => 'ccan', 'CDE02G3009' => 'cde', 'CDE04G3355' => 'cde', 'Cfa005514' => 'cfa', 'Cfa011318' => 'cfa', 'Cfa011438' => 'cfa', 'Cfa021673' => 'cfa', 'Ciclev10001547m.g' => 'ccl', 'Ciclev10028726m.g' => 'ccl', 'CiPaw.05G207800' => 'cil', 'CiPaw.06G146800' => 'cil', 'CiPaw.14G073000' => 'cil', 'ClCG00G006250' => 'cla', 'ClCG02G003490' => 'cla', 'ClCG02G021660' => 'cla', 'ClCG05G009640' => 'cla', 'ClCG05G009650' => 'cla', 'ClCG05G009660' => 'cla', 'ClCG06G003670' => 'cla', 'ClCG07G004470' => 'cla', 'ClCG09G004710' => 'cla', 'ClCG09G010240' => 'cla', 'ClCG09G010500' => 'cla', 'ClCG09G010510' => 'cla', 'ClCG11G004550' => 'cla', 'COL.COLO4_11786' => 'col', 'COL.COLO4_11788' => 'col', 'COL.COLO4_15237' => 'col', 'COL.COLO4_18435' => 'col', 'Cpa.g.sc113.55' => 'cpa', 'Cpa.g.sc252.17' => 'cpa', 'CsaV3_3G019060' => 'csa', 'CsaV3_3G019070' => 'csa', 'CsaV3_7G024040' => 'csa', 'CsaV3_7G025820' => 'csa', 'CsaV3_7G026650' => 'csa', 'CSS0009220' => 'camsi', 'CSS0019370' => 'camsi', 'CSS0028884' => 'camsi', 'DCAR_003340' => 'dca', 'DCAR_015274' => 'dca', 'DCAR_015597' => 'dca', 'DCAR_018879' => 'dca', 'DCAR_018880' => 'dca', 'Dinv01371' => 'din', 'Dinv10038' => 'din', 'Dinv19370' => 'din', 'Dinv19371' => 'din', 'Dinv24288' => 'din', 'Dinv24289' => 'din', 'Dinv24290' => 'din', 'Dinv26278' => 'din', 'Dinv32854' => 'din', 'Duzib168G1598' => 'dzi', 'Duzib170G0680' => 'dzi', 'Duzib248G0867' => 'dzi', 'ECA234G0850' => 'eca', 'ECA240G3985' => 'eca', 'ECA248G1293' => 'eca', 'ECA248G3587' => 'eca', 'EL10Ac5g11042' => 'bvu', 'EL10Ac7g15955' => 'bvu', 'EL10Ac7g15956' => 'bvu', 'EL10Ac7g16943' => 'bvu', 'Eucgr.J02080' => 'egr', 'Eucgr.J02083' => 'egr', 'Eucgr.J02085' => 'egr', 'FAN01G3053' => 'fan', 'FAN08G2206' => 'fan', 'FAN11G1169' => 'fan', 'FAN11G1606' => 'fan', 'FAN13G2588' => 'fan', 'FAN15G2078' => 'fan', 'FAN16G0955' => 'fan', 'FAN18G2751' => 'fan', 'FAN20G0351' => 'fan', 'FAN21G0616' => 'fan', 'FAN21G2091' => 'fan', 'FAN25G2086' => 'fan', 'FAN27G1848' => 'fan', 'FvH4_2g37390' => 'fve', 'FvH4_2g37420' => 'fve', 'FvH4_3g34830' => 'fve', 'FvH4_3g34840' => 'fve', 'FvH4_5g29270' => 'fve', 'Glyma.05G169100' => 'gma', 'Glyma.05G169200' => 'gma', 'Glyma.08G127600' => 'gma', 'Glyma.11G143800' => 'gma', 'Glyma.11G144300' => 'gma', 'Glyma.12G066900' => 'gma', 'Glyma.15G042100' => 'gma', 'Gohir.A03G000051' => 'ghi', 'Gohir.A03G038000' => 'ghi', 'Gohir.A04G121100' => 'ghi', 'Gohir.A13G151600' => 'ghi', 'Gohir.D03G130400' => 'ghi', 'Gohir.D03G172800' => 'ghi', 'Gohir.D04G164000' => 'ghi', 'Gohir.D13G156000' => 'ghi', 'Gorai.003G137100' => 'gra', 'Gorai.003G183500' => 'gra', 'Gorai.012G152000' => 'gra', 'Gorai.013G176600' => 'gra', 'GSVIVG01022896001' => 'vvi', 'GSVIVG01022898001' => 'vvi', 'GSVIVG01022899001' => 'vvi', 'GSVIVG01022901001' => 'vvi', 'GSVIVG01022902001' => 'vvi', 'GSVIVG01022907001' => 'vvi', 'GSVIVG01022913001' => 'vvi', 'GSVIVG01022914001' => 'vvi', 'GSVIVG01022916001' => 'vvi', 'GSVIVG01025045001' => 'vvi', 'GSVIVG01030613001' => 'vvi', 'HanXRQChr01g0010021' => 'han', 'HanXRQChr01g0013191' => 'han', 'HanXRQChr03g0070511' => 'han', 'HanXRQChr03g0073551' => 'han', 'HanXRQChr03g0073561' => 'han', 'HanXRQChr03g0073571' => 'han', 'HanXRQChr03g0073581' => 'han', 'HanXRQChr14g0437431' => 'han', 'Haze_01700' => 'cav', 'Haze_23829' => 'cav', 'Haze_24020' => 'cav', 'Hma1.2p1_0002F.1_g002630' => 'hma', 'Hma1.2p1_0178F.1_g079050' => 'hma', 'Hma1.2p1_0217F.1_g092100' => 'hma', 'Hma1.2p1_0217F.1_g092110' => 'hma', 'Hma1.2p1_0657F.1_g196920' => 'hma', 'Hma1.2p1_0846F.1_g227690' => 'hma', 'HPP92_019815' => 'vpl', 'Hund05011' => 'sun', 'Hund05012' => 'sun', 'Lalb_Chr13g0295711' => 'lal', 'Lalb_Chr14g0374951' => 'lal', 'Lalb_Chr22g0350021' => 'lal', 'Lj1C161T8' => 'lonja', 'Lj2A1051T20' => 'lonja', 'Lj3g0000451' => 'lja', 'Lj3g0017384' => 'lja', 'Lj3g0019181' => 'lja', 'Lj4g0007048' => 'lja', 'Lj4g0016798' => 'lja', 'Lj4g0027958' => 'lja', 'Lj9A304G86' => 'lonja', 'Lj9A304T88' => 'lonja', 'Lj9A304T89' => 'lonja', 'Lj9A305G44' => 'lonja', 'Lj9C305G1' => 'lonja', 'Lsat_1_v5_gn_5_105420' => 'lsa', 'Lsat_1_v5_gn_5_166580' => 'lsa', 'Manes.10G128400' => 'mes', 'Manes.10G128500' => 'mes', 'Manes.11G135200' => 'mes', 'Manes.11G135300' => 'mes', 'Manes.11G135400' => 'mes', 'Mapoly0001s0185' => 'mpo', 'MBI05_g07854_MAGBIO' => 'mbi', 'MBI08_g16116_MAGBIO' => 'mbi', 'MD03G1100900' => 'mdo', 'MD08G1231900' => 'mdo', 'MD08G1232200' => 'mdo', 'MD08G1232300' => 'mdo', 'MD11G1115000' => 'mdo', 'Medtr4g032360' => 'mtr', 'Medtr4g062550' => 'mtr', 'Medtr4g062570' => 'mtr', 'Medtr4g072780' => 'mtr', 'Medtr4g076710' => 'mtr', 'Medtr5g022720' => 'mtr', 'Medtr7g033690' => 'mtr', 'Medtr8g088860' => 'mtr', 'Medtr8g088880' => 'mtr', 'Medtr8g088890' => 'mtr', 'MELO3C019469.2' => 'cme', 'MELO3C019470.2' => 'cme', 'MELO3C023702.2' => 'cme', 'Migut.B00831' => 'egut', 'Migut.D02137' => 'egut', 'Migut.L00366' => 'egut', 'Migut.L00532' => 'egut', 'Migut.L00533' => 'egut', 'Migut.L00534' => 'egut', 'Migut.L00535' => 'egut', 'Migut.L00536' => 'egut', 'Migut.L00592' => 'egut', 'Migut.L01247' => 'egut', 'Migut.L01248' => 'egut', 'MSTRG.18599' => 'ama', 'Nitab4.5_0000610g0210' => 'nta', 'Nitab4.5_0003179g0050' => 'nta', 'Nitab4.5_0005009g0010' => 'nta', 'Nitab4.5_0006123g0050' => 'nta', 'Nn2g13715' => 'nnu', 'Nn4g24739' => 'nnu', 'Nn4g24741' => 'nnu', 'Oeu010009.1' => 'oeu', 'Oeu013947.1' => 'oeu', 'Oeu041007.1' => 'oeu', 'Oeu062315.1' => 'oeu', 'Os01g0976200' => 'osa', 'Os05g0116000' => 'osa', 'Os09g0552500' => 'osa', 'Os09g0552600' => 'osa', 'Peaxi162Scf00004g00357' => 'pax', 'Peaxi162Scf00011g00430' => 'pax', 'Peaxi162Scf00123g00067' => 'pax', 'Peaxi162Scf00390g00014' => 'pax', 'Peaxi162Scf00406g00134' => 'pax', 'PGR042G3044' => 'pgr', 'PGR119G2440' => 'pgr', 'PGSC0003DMG400000013' => 'stu', 'PGSC0003DMG400000015' => 'stu', 'PGSC0003DMG400000016' => 'stu', 'PGSC0003DMG400015539' => 'stu', 'PGSC0003DMG400015564' => 'stu', 'PGSC0003DMG400023762' => 'stu', 'PGSC0003DMG400023764' => 'stu', 'PGSC0003DMG400037886' => 'stu', 'Phvul.002G239800' => 'pvu', 'Phvul.002G239900' => 'pvu', 'Phvul.002G249800' => 'pvu', 'Phvul.011G067800' => 'pvu', 'Phvul.L001743' => 'pvu', 'Potri.001G402600' => 'ptr', 'Potri.007G047200' => 'ptr', 'Potri.008G102900' => 'ptr', 'Prupe.1G570700' => 'ppe', 'Prupe.1G570800' => 'ppe', 'Prupe.6G085800' => 'ppe', 'Prupe.6G085900' => 'ppe', 'Psat7g061760' => 'psa', 'Psat7g061840' => 'psa', 'Psat7g219040' => 'psa', 'PSO063G1097' => 'pso', 'PSO210G5582' => 'pso', 'PSO339G0611' => 'pso', 'PSO541G1070' => 'pso', 'PSO566G0284' => 'pso', 'PSO675G8832' => 'pso', 'PSO782G5363' => 'pso', 'PSO832G3637' => 'pso', 'QL01p033573' => 'qlo', 'QL02p098808' => 'qlo', 'QL02p098827' => 'qlo', 'QL02p098852' => 'qlo', 'QL02p098859' => 'qlo', 'QL02p098877' => 'qlo', 'QL02p098895' => 'qlo', 'QL12p016724' => 'qlo', 'QL12p016755' => 'qlo', 'RcHm_v2.0_Chr4g0444011' => 'rch', 'RcHm_v2.0_Chr5g0062671' => 'rch', 'RcHm_v2.0_Chr5g0062681' => 'rch', 'RcHm_v2.0_Chr6g0304301' => 'rch', 'RcHm_v2.0_Chr7g0185521' => 'rch', 'RcHm_v2.0_Chr7g0198921' => 'rch', 'RcHm_v2.0_Chr7g0198931' => 'rch', 'RcHm_v2.0_Chr7g0222091' => 'rch', 'RcHm_v2.0_Chr7g0222101' => 'rch', 'Rhsim01G0224200' => 'rsi', 'Rhsim09G0048800' => 'rsi', 'Rhsim11G0128900' => 'rsi', 'Rhsim11G0129000' => 'rsi', 'Sabra07G0042100' => 'sbr', 'Sabra08G0077800' => 'sbr', 'Sabra10G0114200' => 'sbr', 'Sabra16G0264100' => 'sbr', 'Sabra16G0264200' => 'sbr', 'SalBow1G8341' => 'sbo', 'SalBow2G1762' => 'sbo', 'SalBow3G1675' => 'sbo', 'Sc10g0009840' => 'sci', 'Sc10g0009870' => 'sci', 'Sc20g0006170' => 'sci', 'Sed0006525' => 'sed', 'Sed0009089' => 'sed', 'Sed0013563' => 'sed', 'Sed0015026' => 'sed', 'Sed0024130' => 'sed', 'Sed0025471' => 'sed', 'Sed0026978' => 'sed', 'SEGI_11657' => 'sgi', 'SGA_v2.0_scaffold14G07007' => 'sas', 'SGA_v2.0_scaffold338G49206' => 'sas', 'SGA_v2.0_scaffold36G14421' => 'sas', 'SGA_v2.0_scaffold455G51910' => 'sas', 'SGA_v2.0_scaffold4747G54527' => 'sas', 'SMO012G0021' => 'smo', 'SMO169G0148' => 'smo', 'SMO199G0011' => 'smo', 'SMO201G0181' => 'smo', 'SMO329G0086' => 'smo', 'SMO353G0404' => 'smo', 'SMO358G0588' => 'smo', 'SMO361G0211' => 'smo', 'Solyc01g094110.3' => 'sly', 'Solyc01g104100.3' => 'sly', 'Solyc01g104110.4' => 'sly', 'Solyc11g073200.2' => 'sly', 'Solyc11g073210.2' => 'sly', 'Sopen01g046510' => 'spe', 'Sopen01g046520' => 'spe', 'Sopen01g046530' => 'spe', 'Sopen01g046540' => 'spe', 'Sopen01g046550' => 'spe', 'Sopen11g030830' => 'spe', 'Sopen11g030840' => 'spe', 'Sp4g02870' => 'spa', 'Sp4g11550' => 'spa', 'TAR092G0002' => 'tar', 'TAR633G1144' => 'tar', 'TAR636G2197' => 'tar', 'TAR636G2361' => 'tar', 'THA.LOC104800641' => 'tha', 'Thecc.02G087400' => 'tca', 'Thecc.09G328800' => 'tca', 'Thhalv10008034m.g' => 'esa', 'Thhalv10016860m.g' => 'esa', 'TPR.G1010' => 'tpr', 'TPR.G19965' => 'tpr', 'TPR.G20513' => 'tpr', 'TPR.G23091' => 'tpr', 'TPR.G23093' => 'tpr', 'TPR.G23097' => 'tpr', 'TPR.G23099' => 'tpr', 'TWI32G0489' => 'twi', 'TWI75G1744' => 'twi', 'TWI75G1799' => 'twi', 'TWI79G1699' => 'twi', 'unitig_8.g3458' => 'ugi', 'unitig_8.g3459' => 'ugi', 'unitig_899.g15435' => 'ugi', 'unitig_899.g15436' => 'ugi', 'vmacro01758' => 'vma', 'vmacro01759' => 'vma', 'vmacro14501' => 'vma', 'VMungo0251G2085' => 'vmu', 'VMungo0251G2685' => 'vmu', 'VMungo0251G3046' => 'vmu', 'VMungo0251G3585' => 'vmu', 'VMungo0464G1510' => 'vmu', 'VMungo1080G1273' => 'vmu', 'VMungo1127G0475' => 'vmu', 'VMungo1309G0287' => 'vmu', 'Zm00001eb132730' => 'zma', 'Zm00001eb266290' => 'zma', 'Zm00001eb355570' => 'zma', 'Zm00001eb401380' => 'zma' ) $gf_id = 'HOM05D001223' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001223' ) $data_identifier = 'HOM05D001223' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 1, 'aag' => (int) 39, 'ach' => (int) 11, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 5, 'cqu' => (int) 11, 'bca' => (int) 10, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 17, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 13, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 11, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 6, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 3, 'egut' => (int) 11, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 5, 'smo' => (int) 8, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 2, 'tar' => (int) 4, 'tha' => (int) 1, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401380' $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